ChIP-Atlas: SRX11976463

Antigen

Cell type Class: Neural
Cell type: Cerebral Cortex
MeSH Description: Type of cerebral cortex which does not pass through a perinatal phase of six-layered structure as in the NEOCORTEX and develops into three or four layers in the mature brain. Allocortex has three subareas: archi- paleo- and periallo-cortex.

library_strategy: ChIP-Seq
library_source: GENOMIC
library_selection: ChIP
library_construction_protocol: Nuclear extracts were prepared from sorted cells and digested with MNase to obtain mono- and di-nucleotide fragments. Digested chromatin was dialysed overnight. Input control chromatin was set aside, and immunoprecipitation reactions were performed with antibodies against H3K27ac (Abcam, ab472) or H3K27me3 (Active motif, 39157). Precipitated fractions were purified using Dynabeads (Invitrogen) and RNase-treated prior to library construction. Libraries were prepared using an Ovation Ultralow DR Multiplex System (Nugen), size selected in the range of 180-300 bp on a BluePippin (Sage Science), quality control tested on a Bioanalyzer (Agilent) and sequenced on a HiSeq 4000 (Illumina). Nuclear extracts were prepared from cells and sheared using a bioruptor (18-40 cylces; 30s ON and 45s OFF). Input control chromatin was set aside, and immunoprecipitation reactions were performed with antibodies against the relevant TF or IgG or a blocking peptide overnight at 4C. Precipitated fractions were purified using Dynabeads (Invitrogen) and RNase-treated prior to library construction. Libraries were prepared using an Ovation Ultralow DR Multiplex System (Nugen), size selected in the range of 180-300 bp on a BluePippin (Sage Science), quality control tested on a Bioanalyzer (Agilent) and sequenced on a HiSeq 4000 (Illumina).